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(topology analysis). This allows the identification of important biological functions or

functional network proteins (potential therapeutic targets), which can then be further char­

acterized and experimentally validated.

The network created can then be examined in more detail later on, e.g. to understand

intercellular networks and communication (what goes wrong in the network so that a

tumour develops; what is a potential drug target). It can also be used for dynamic model­

ling (in silico simulation) to better understand the behaviour of the network, e.g. what

happens after an infection or what effect does a drug have?

Example 5.6

Correct is B and D. To find all human interaction partners for BRCA1, you should enter

BRCA1 as the search term and search, then select human as the organism.

Question 5.7

To do this, you need to reconstruct a network (e.g. STRING and KEGG databases), then

load the network (e.g. as a .sif file) into Cytoscape and examine it with the BiNGO plugin

(alternatively also ClueGO plugin) (see also previous answers).

Example 5.8

Answer A.

20.5

Example 5.9

Answer B, C.

BiNGO identifies overrepresented biological functions (with p-value and correspond­

ing genes), so-called Gene Ontology (GO), in a network (https://www.ncbi.nlm.nih.gov/

pubmed/15972284). In the GO groups, genes are grouped according to their species-­

specific known function into the categories of biological processes, cellular component

and molecular function (https://www.geneontology.org/). One can thus find all processes

involved for the network, which allows one to detect, for example, functions and proteins

involved specifically for a process, such as the cell cycle. From this, one can then in turn

create a subnetwork of all proteins for this process and investigate it in detail. In this case,

the BiNGO analysis shows a large number of biological processes (well over 100), includ­

ing BRCA1 involvement in the cell cycle checkpoint (GO-ID 75).

Question 5.10

A Gene Ontology is a species-specific functional grouping (biological process, cellular

component and molecular function) of genes (term). Allows a functional annotation (see

also question 5.9).

Example 5.11

Answer A, C, E.

20  Solutions to the Exercises